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Jupyter Notebook: viewer tool for pseudoatomic models fitting into cryo-EM electrondensity maps of lattice based DNA origami structures

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License: GPL v3 Python-version: | FitViewer | Usage | Requirements | References

FitViewer

FitViewer for context based zoning and cropping of cryo-EM maps using pseudo-atomic models fitting into cryo-EM electron density maps of lattice based DNA origami structures

Usage

start the interactive Jupyter-Notebook by executing the following command from the repository directory:

jupyter notebook viewertool.ipynb

Step by step instructions are provided in the Jupyter notebook

Requirements

FitViewer is currently distributed as a Jupyter Notebook. It requires an ipytohn kernel with the following dependencies:

python >= 3.8.0

dnaFit DNA Origami atomic model package

required PyPI packages:

ipywidget
ipython
jupyter

Supported formats

FitViewer relies on the MDAnalysis package for reading trajectories or coordinate files, mrcfile for handling cryo-EM data, and DNA Origami design files generated using cadnano

References

When using FitViewer in published work, please cite the following paper:

Kube, M., Kohler, F., Feigl, E. et al. Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution. Nat Commun 11, 6229 (2020). https://doi.org/10.1038/s41467-020-20020-7

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Jupyter Notebook: viewer tool for pseudoatomic models fitting into cryo-EM electrondensity maps of lattice based DNA origami structures

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